Looking at adding the ability to have supplemental panels via the DC jack while wiring in my primary panels with the mini USB cable.

It is fine for the charger, but you need to make sure your panels are protected. If the panels are mis-matched, or one panel becomes 'shaded', power from the other one can back up through it. At best it will be horribly inefficient. At worst, it can damage the panel. Best to do a bit of research before you start connecting multiple panels.

My design revolves around wiring "identical" panels in parallel to each other. Is this still a concern with individual panels being shaded? Also, between the panels and the charging circuit, do I need to include some sort of diode if I plan on using both input ports at once?

Two part question. I notice on the LiPo board there is one additional DC IN next to the Mini USB. If I wire the AA/AAA Joule Thief to this input (or similar connector: USB/DC), will it appropriately transfer what's left from the AA/AAA to the LiPo via the charging circuit? I'm not quite sure how to work out how the small amounts of power left in the AA/AAA will affect the circuit overall and subsequently the charging of the LiPo (specifically the required voltage).

SEEMS like it should work since you can regulate the output onboard between 3.3 and 5v.

It you set the output to 5v, it should be able to transfer some of the remaining AA charge into the LiPo. Just don't connect it at the same time as the USB.

Is this a precaution because of energy flowing back into the extra device or the LiPo circuit itself? I believe we've discussed elsewhere that you can have both multiple inputs as long you have the appropriate diodes in place for back flow.

Also, after speaking with the developer of the AASaver, he suggested that limiting the LiPo circuit to 100mA would be more efficient while transferring whatever juice is left in the AA/AAAs. Any insight into this? I planned on wiring in the additional 1000ohm resistor to bump the charging circuit up to 1000mA from 500mA.

In regards to the information regarding adding a new resistor, are we removing the on-board resistor in place by desoldering from PROG? The guide speaks of soldering OVER the in place resistor, so I assume this would be the case.

Is this a precaution because of energy flowing back into the extra device or the LiPo circuit itself?

It is so you don't have two voltage regulators trying to regulate the same circuit.

In regards to the information regarding adding a new resistor, are we removing the on-board resistor in place by desoldering from PROG? The guide speaks of soldering OVER the in place resistor, so I assume this would be the case.

The formula for the programming resistor is based on the total resistance. If you solder one in parallel with the existing resistor, you need to calculate the effective total resistance = (R1 * R2) / (R1 + R2)